When you create a custom report under Reports Menu >> Manage Custom Reports, you can choose specific pay categories to be included in the report. After you initially create the report, if you return to Manage Custom Reports to make an adjustment to the report, the Pay Categories defaults back to all, and you must go through and reselect the specific categories you want included.
My clients and I would prefer if the Custom Report would maintain this data, so you can add/remove fields from the report without needing to choose the categories each time.